The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility

Significance Statement

SREBP signaling regulates transcriptions of genes necessary for the homeostasis of fatty acids and cholesterol in the cell, which is a key factor for cellular wellbeing and proliferation. Accordingly, the abrogation of SREBP signaling is associated with numerous pathological conditions ranging from cardiometabolic disorders to metabolic syndrome and cancer. Representing many other signaling processes from homeostasis to proliferation, compartmentalization, and differentiation like Wnt and Notch, the signal cascade is elicited via a regulated intramembrane proteolysis (RIP), i. e. the proteolytic cleavage of a membrane-integral transcription factor. In this work, Linser et al. find that the membrane-spanning part of the SREBP transcriptional activator precursor molecule, which is the substrate in the RIP process, comprises interrupted structural stability. This enables conformational flexibility and maybe one of the factors explaining the enigmatic specificity and selectivity of the eminent and evolutionarily conserved RIP process, which is poorly understood to-date.

About the author

Dr. Rasmus Linser obtained his PhD in Biophysics at the Leibniz Institute for Molecular Pharmacology in Berlin, Germany, in 2010. During his postdoctoral studies, he worked at the University of New South Wales in Sydney, Australia, and Harvard Medical School, Boston, MA, developing and using Nuclear Magnetic Resonance (NMR) spectroscopic methods both in the solution and solid state. His independent group, which he started in 2014 at the Max Planck Institute for biophysical chemistry in Göttingen, is concerned with the development and application of NMR methods mostly for solid proteins. With these, the molecular mechanisms of disease-related or functional amyloids, membrane proteins, and enzymes are characterized from a structural point of view and concerning protein dynamics. This helps to shed light on the various mechanisms that cells have invented to survive. Dr. Linser’s lab is currently funded by the German Research Association (DFG, Emmy Noether program and SFB 803, project A03), the Association of the Chemical Industries (VCI), and the Michael J. Fox Foundation.

About the author

Prof. Dr. Gerhard Wagner obtained his PhD in Biophysics at the Eidgenössische Technische Hochschule (ETH) in Zürich, Switzerland, in 1977. After postdoctoral work at the Massachusetts Institute of Technology (MIT) in Cambridge, MA and the ETH, he accepted an Associate Professor position at the University of Michigan in 1987. Since 1990, he has been a Professor (since 1992 Elkan Rogers Blout Professor) at Harvard Medical School, Boston, MA, in the Department of Biological Chemistry and Molecular Pharmacology. He has been awarded with numerous high-rank honors and has been elected a member of various associations, including the German Academy of Sciences (Leopoldina), the National Academy of Sciences of the United States and the American Academy of Arts and Sciences. His lab has been pivotal regarding the development and application of solution NMR methods. The approaches developed in the Wagner lab have been leading the way to characterization of structure and function of proteins in solution by NMR spectroscopy, for example with regard to the elucidation of eukaryotic translation initiation. Dr. Wagner’s lab is funded by the National Institute of Health (NIH) with grants GM046476 and HL116391.

Figure Legend: Dynamics of the substrate, enabled by interrupted structural definition, may play a role for the specificity in Regulated Intramembrane Proteolysis. Many molecular details of this evolutionarily conserved mechanism are still enigmatic, even though it is a constituent of numerous signaling cascades. This work was pursued in the case of SREBP signaling, which is a hallmark of numerous pathological conditions from cardiometabolic disorders to cancer.

Journal Reference

Proc Natl Acad Sci U S A. 2015;112(40):12390-5.

Linser R¹, Salvi N², Briones R³, Rovó P⁴, de Groot BL³, Wagner G⁵.

[expand title=”Show Affiliations”]

Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; [email protected] [email protected]
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; Université Grenoble Alpes, Centre National de la Recherche Scientifique, and Commissariat à l’Énergie Atomique et aux Énergies Alternatives, Institut de Biologie Structurale, F-38044 Grenoble, France;
Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
Department NMR-Based Structural Biology, Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany;
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; [email protected] [email protected] [/expand]

Abstract

Regulated intramembrane proteolysis (RIP) is a conserved mechanism crucial for numerous cellular processes, including signaling, transcriptional regulation, axon guidance, cell adhesion, cellular stress responses, and transmembrane protein fragment degradation. Importantly, it is relevant in various diseases including Alzheimer’s disease, cardiovascular diseases, and cancers. Even though a number of structures of different intramembrane proteases have been solved recently, fundamental questions concerning mechanistic underpinnings of RIP and therapeutic interventions remain. In particular, this includes substrate recognition, what properties render a given substrate amenable for RIP, and how the lipid environment affects the substrate cleavage. Members of the sterol regulatory element-binding protein (SREBP) family of transcription factors are critical regulators of genes involved in cholesterol/lipid homeostasis. After site-1 protease cleavage of the inactive SREBP transmembrane precursor protein, RIP of the anchor intermediate by site-2 protease generates the mature transcription factor. In this work, we have investigated the labile anchor intermediate of SREBP-1 using NMR spectroscopy. Surprisingly, NMR chemical shifts, site-resolved solvent exposure, and relaxation studies show that the cleavage site of the lipid-signaling protein intermediate bears rigid α-helical topology. An evolutionary conserved motif, by contrast, interrupts the secondary structure ∼9-10 residues C-terminal of the scissile bond and acts as an inducer of conformational flexibility within the carboxyl-terminal transmembrane region. These results are consistent with molecular dynamics simulations. Topology, stability, and site-resolved dynamics data suggest that the cleavage of the α-helical substrate in the case of RIP may be associated with a hinge motion triggered by the molecular environment.

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